Hi Rocky welcome back to the fold! A lot has changed in this (the dirt world) in the past 25 years. I was an avid rider/racer back (and am today) then so I get to speak from experience. I remember the days of yesteryear when whooped out trails were non existent (yes folks this really was the case) and you could take a bike with the standard 4" of travel suspention and have a blast. Rocky those days are gone FOREVER (at least here in Mi). What we have now is a "trail system" that requires us to "stay on the trail or suffer the consequenses". This, in turn, has pushed ALL of us woods/trail rippers (using your own words) into a realitively small environment which in turn suffers the consequences (whoops, sand, treachourus high speed two way traffic andthe like).
I tell you all this for one reason - it supports my response to your main question. Honda has chosen to leave the XR400 virtually unchanged since conception. Compared to the Yam, it is a heavy/cumbersome/WAY under suspended trail bike that really should not be listed in the same category as the Yam WR/YZF! Yamaha on the other hand has continued to update their WR (in my opinion this shows continued seriousness on there part) to make it a very competitive machine without losing the "trail riding" side.
When you say "rip" I interpret that as "rip". As in, "hey Joe - watch me rip up that set of whoops in the trail". Is this correct?? If so, I promise you that you will not "rip" on an XR - you will "anti-rip" at the first good section of whoops that you come to - GUARENTEED! Even if you do attempt that "rip" the XR will "attempt" to throw you off its back into on coming traffic (a real possibility). Again, HONDA has NOT done the followup and equiped the XR400 to accomplish this! Yamaha has!
I have owned and ridden BOTH and I am telling you the way it REALLY is!
I will leave the rest of your question for others (maintenance, LC vrs AIR cooling, resale values and the like) but I will finish with this thought. The Honda XR was a GREAT trail bike in its day, but current Michigan trail conditions really limit its "fun for dollar" value compared to other even GREATER machines out there (Yamaha, KTM, Kawasaki, Gas Gas, VOR ect.) like the mighty CRF450!
Doggonit, I thought I could get thru one of these disortations without mentioning my Christmas dream.........
Woodsy